~ It's a long way from Amphioxus

Using LiftOver to convert genome assembly coordinates

Suppose we have two different assemblies of the same organism, G1.fasta and G2.fasta, and we want to know the which regions in G2 correspond to our interested regions in G1, what should we do? UCSC LiftOver is a great tool to solve this kind of problems and here is how>

The blat command usually take two arguments, the first is the database while the second is the query sequence. So in general, you would want to use the larger genome (or more continuous one) as the database and use the other as the query to make the homologous search more efficient. In general, we would like to search against the whole genome rather than a specific chromosome because 1) usually you might not necessarily know which chromosome your query sequence correspond to and 2) we want to account for potential interchromosomal rearrangements such as translocations. So in general, searching against the whole genome is a safer bet. I’ve used this method for converting genome coordinates between two metazoan genomes (genome size = ~500 Mb), so running it for human should not be a problem. For sure it will take longer computational time and consume more RAM and storage space though. :-)